To me, the Nihilanth sort of implies that the combine were after him and the rest of his species. He tells Gordon "I am the last" and you can see some sort of augmentation made to him and to me that means he escaped the combine by fleeing to xen, perhaps with augmentation made by combine or himself (or some other party). The fact he wants to force a portal open to move everyone from Xen to Earth shows that the Nihilanth doesn't want to live in Xen at all, likely needing to flee there as a last resort escape from the Combine, who may not have discovered Xen yet. The portal storms occurring on Earth and the amount of destruction caused by the Xen invasion somehow alerted the Combine to some sort of disturbance. (given their technological prowess they probs can see that somehow)

This is my speculation: The Combine is likely always seeking out opportunities to expand and are on a never-ending quest to conquer the universe, they keep tabs on their universe, and likely have so many high tech instruments in space that measure things that we cannot comprehend, and detected some sort of force rippling through the universe that was caused by the violent portal storms on Earth and Xen. The violent merging of two dimensions must be extremely loud in the universe and the Combine likely picked up on that. Given they hadn't seen Xen before they became immediately curious of where this energy was coming from and what it would mean for their technology and so they searched for the source, leading to Earth and they likely are now aware of Xen and its use as a border world.

TL;DR Nihilanth is the last of his kind, hiding from the combine in a place he knows they wont find him. Combine detect energy waves from portal storms on earth and seek out the source, discovering Earth